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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2hvd ADP Nucleoside diphosphate kinase A 2.7.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 1.030
4uoh ADPNucleoside diphosphate kinase / 0.830
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.804
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.803
4uof DATNucleoside diphosphate kinase / 0.801
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.791
4uog YYYNucleoside diphosphate kinase / 0.760
4fkx CDPNucleoside diphosphate kinase / 0.759
2az3 CDPNucleoside diphosphate kinase / 0.756
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.746
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.742
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.729
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.715
3q8u ADPNucleoside diphosphate kinase / 0.702
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.678
3b1p NOSPfkB carbohydrate kinase family protein / 0.674
1qmf KEFPenicillin-binding protein 2x / 0.671
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.669
5cns CDPRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.663
3nd1 SAHPrecorrin-6A synthase (Deacetylating) / 0.660
3au2 DGTDNA polymerase beta family (X family) / 0.658
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.655
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.654
3ngu ADPNucleoside diphosphate kinase / 0.654
4a39 GEMUncharacterized protein / 0.653
2rdn 1PL1-deoxypentalenic acid 11-beta-hydroxylase 1.14.11.35 0.652